I'm surprised to find more than forty rank between Nadal and Federer. I think the reasoning behind their ranking is not consistent. Here is why:

Federer had great results on clay: He has a leading H2H against the clay court specialist of the the early 00's like Coria, Moya or Ferrero. He has a top 10 winning percentage on clay. He has won RG once, and reached 4 finals. He won six clay master 1000, and reached 8 clay master 1000 finals. If not for one man, he would have an amazing clay palmares and winning percentage. These points are indisputable.

From here there is two possibilities:

1) He was prevented to win so much on clay by the best clay-courter ever. Despite his lack of titles on clay in comparison with other, he has to be considered higher than others who didn't have to face such an opposition (Kuerten, Agassi, Muster, in recent times). He is in this case at least a top 10 of the open era, not far all-time.

2) His opposition was weak, very weak (and there is some point in this direction, although I believe it is more complicated than that), and thus his amazing accomplishments don't compare with others, like Kuerten, Muster, Agassi, who had a far greater opposition: Federer is not a great clay courter: he played in the weaker clay era ever.

It seems that in this thread it is the second hypothesis which has been chosen. Then, how in hell can Nadal be ranked number 1? Nadal did his harvest in the exact same time span than Federer. If it is considered that Federer's accomplishment can't be taken into account because his opposition was weak, then it has to be the same for Nadal's accomplishment, for the sake of coherence! In that case, despite the fact that Nadal has won many more majors than Lendl or Wilander, many more master 1000, and has a higher winning percentage than them, why not rank him below them? Or below anyone else?

Can someone explain me the coherence of ranking these to guys so far from each others, when one win everything and the other was runner-up of everything?

I can't really judge the pre open era players. But judging by Federer's position in the list among open era players, his position does not seem unreasonable. Top 10 and in very good company